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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
France
Argentina
Germany
Iran
Spain
Indonesia
Poland
South Africa
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Hungary
Philippines
Canada
Belgium
Pakistan
Bangladesh
Bulgaria
Iraq
Netherlands
Tunisia
Bolivia
Portugal
Egypt
Japan
Sweden
Paraguay
Greece
Slovakia
Switzerland
Austria
Guatemala
Jordan
Bosnia and Herzegovina
Nepal
Morocco
Croatia
Saudi Arabia
Lebanon
Malaysia
Honduras
Serbia
Panama
Israel
Afghanistan
Moldova
Burma
Uruguay
Georgia
North Macedonia
Kazakhstan
Ireland
Azerbaijan
Costa Rica
China
Armenia
Slovenia
Lithuania
Ethiopia
Algeria
Sri Lanka
Dominican Republic
Kenya
Thailand
West Bank and Gaza
Oman
Venezuela
Belarus
Libya
Zambia
Zimbabwe
Sudan
Namibia
Latvia
Denmark
El Salvador
Uganda
Albania
Kosovo
Kuwait
Kyrgyzstan
Cuba
Nigeria
South Korea
United Arab Emirates
Syria
Montenegro
Malawi
Bahrain
Botswana
Cameroon
Estonia
Senegal
Mozambique
Cambodia
Jamaica
Congo (Kinshasa)
Trinidad and Tobago
Finland
Angola
Madagascar
Australia
Luxembourg
Ghana
Uzbekistan
Norway
Taiwan*
Somalia
Mongolia
Eswatini
Rwanda
Suriname
Qatar
Mali
Mauritania
Guyana
Haiti
Malta
Cyprus
Vietnam
Lesotho
Belize
Cote d'Ivoire
Cabo Verde
Bahamas
Maldives
Hong Kong
Guinea
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Fiji
Djibouti
Togo
Andorra
South Sudan
Tajikistan

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Peru
Russia
United Kingdom
Italy
Colombia
France
Argentina
Germany
Iran
Spain
Indonesia
Poland
South Africa
Ukraine
Turkey
Chile
Romania
Ecuador
Czechia
Hungary
Philippines
Canada
Belgium
Pakistan
Bangladesh
Bulgaria
Iraq
Netherlands
Tunisia
Bolivia
Portugal
Egypt
Japan
Sweden
Paraguay
Greece
Slovakia
Switzerland
Austria
Guatemala
Jordan
Bosnia and Herzegovina
Nepal
Morocco
Croatia
Saudi Arabia
Lebanon
Malaysia
Honduras
Serbia
Panama
Israel
Afghanistan
Moldova
Burma
Uruguay
Georgia
North Macedonia
Kazakhstan
Ireland
Azerbaijan
Costa Rica
China
Armenia
Slovenia
Lithuania
Ethiopia
Algeria
Sri Lanka
Dominican Republic
Kenya
Thailand
West Bank and Gaza
Oman
Venezuela
Belarus
Libya
Zambia
Zimbabwe
Sudan
Namibia
Latvia
Denmark
El Salvador
Uganda
Albania
Kosovo
Kuwait
Kyrgyzstan
Cuba
Nigeria
South Korea
United Arab Emirates
Syria
Montenegro
Malawi
Bahrain
Botswana
Cameroon
Estonia
Senegal
Mozambique
Cambodia
Jamaica
Congo (Kinshasa)
Trinidad and Tobago
Finland
Angola
Madagascar
Australia
Luxembourg
Ghana
Uzbekistan
Norway
Taiwan*
Somalia
Mongolia
Eswatini
Rwanda
Suriname
Qatar
Mali
Mauritania
Guyana
Haiti
Malta
Cyprus
Vietnam
Lesotho
Belize
Cote d'Ivoire
Cabo Verde
Bahamas
Maldives
Hong Kong
Guinea
Papua New Guinea
Congo (Brazzaville)
Burkina Faso
Gabon
Fiji
Djibouti
Togo
Andorra
South Sudan
Tajikistan